Study of Smoking During Pregnancy

flowchart TD
  
  subgraph 01_load
  %%load
  R{{"download_dataset_ncbi"}} -->|"read_unstructured_ncbi_table"| A[ncbi_data]
  T{{"download_data_annotation_ncbi"}} -->|"read_bgx_file"| I[annotation_data]
  
  %%write
  A[ncbi_data] -->|"write_tsv"| B[01_ncbi_data.tsv.gz]
  I["annotation_data$probes"] --> |"write_tsv"| J["01_ncbi_annot_probes.tsv.gz"]
  end
  subgraph 02_clean
  %%ncbi_data pipe
  B[01_ncbi_data.tsv.gz] -->|"read_tsv"| C[ncbi_data]
  C[ncbi_data] -->|"as_tibble |> <br/>filter(!str_detect) |> <br/>slice(41:n) |> <br/>t()"| D[ncbi_dirty_pheno]
  D[ncbi_dirty_pheno] --> |"colnames[1, ] |> <br/>str_replace_all('!sample_', ' ')"| E[ncbi_dirty_pheno]
  E[ncbi_dirty_pheno] --> |"[-1, ] |> <br/>as_tibble() |> <br/>rename_with()"| F[ncbi_dirty_pheno]
  F[ncbi_dirty_pheno] --> |"select() |> <br/>mutate() |> <br/>select() |> <br/>t() |> <br/>as.data.frame() |> <br/>rename_with() |> <br/>as_tibble()"| H[ncbi_clean_pheno]:::red
  
  %%sample source and all of the expr
  H[ncbi_clean_pheno]:::red --> |"select() |> <br/>mutate() |> <br/>rename() |> <br/>select()"| S[sample_source table]
  S[sample_source table] --- U>"get_gene_expr_by_source()"]
  Q["ncbi_clean_expression"] --- U>"get_gene_expr_by_source()"]
  U>"get_gene_expr_by_source()"] --> V[gene_expr_placenta]:::red
  U>"get_gene_expr_by_source()"] --> W[gene_expr_maternal_blood]:::red
  U>"get_gene_expr_by_source()"] --> X[gene_expr_cord_blood]:::red
  
  %%ncbi_dirty_expr pipe
  C[ncbi_data] -->|"slice()"| G[ncbi_dirty_expr]
  G[ncbi_dirty_expr] --> |"colnames() |>  <br/>slice() |>  <br/>unlist()"| L[ncbi_dirty_expr]
  L[ncbi_dirty_expr] --> |"rename() |> <br/>mutate(across(-probe.id, ~ as numeric(.x))) "| M[ncbi_dirty_expr]
  
  %%annotation probe
  J["01_ncbi_annot_probes.tsv.gz"] -->|"read_tsv()"| N["ncbi_annot_probes"]
  N["ncbi_annot_probes"] --> |"select()"| O["gene_annotation"]
  
  %%merging to clean ncbi
  O["gene_annotation"] ---|"select()"| P( ):::empty
  M["ncbi_dirty_expr"] --- P( )
  P( ) -->|"right_join(by = c('Probe_Id' = 'probe_id')) |> <br/>rename() |> <br/>select()"| Q["ncbi_clean_expression"]:::red
  
  classDef red stroke:#f00,stroke-width:3px
  end
  %%writing and reading
  %%subgraph 04_augment
  %%Q["ncbi_clean_expression"] -->  Y[gene_expr_placenta]
  %%V[gene_expr_placenta] -->  Z[gene_expr_placenta]
  %%W[gene_expr_maternal_blood] -->  AA[gene_expr_maternal_blood]
  %%X[gene_expr_cord_blood] -->  AB[gene_expr_cord_blood]
  %%H[ncbi_clean_pheno] -->  AC[ncbi_clean_pheno]
  %%end